Table 2 Array summaries
CompanyArrayProduct InformationaNo. AssaysNo. PositionsPercent Overlap with 1000 GenomesPercent Overlap with 1000 Genomes, MAF Filtered
IlluminaHumanCore12v1-0, A296,720296,67788.287.8
IlluminaHumanCore+Exome12v1-0, B535,743528,48476.369.3
AffymetrixAxiom Biobankna33716,836645,20973.667.7
IlluminaOmniExpress12v1, H727,413727,41098.898.8
AffymetrixAxiom World Array 4na32841,602814,83198.698.5
IlluminaOmni2.5M8v1, A2,368,2182,362,58093.293.0
IlluminaOmni2.5M+Exome8v1, A2,556,8122,513,57891.589.9
IlluminaOmni5M4v1, C4,285,6574,279,79394.493.2
  • Summaries of each array included in these genomic coverage analyses, restricted to assays mapped to chromosomes 1 through 22 and the non-pseudoautosomal portion of the X chromosome. For each array, the columns give (1) the company manufacturing the array; (2) the array name; (3) additional product information; (4) the total number of assays; (5) the total number of unique map locations represented by those assays; (6) the percent overlap with 1000 Genomes phase 1 integrated variant set, at any frequency; and (7) the percent overlap with 1000 Genomes phase 1 integrated variant set, with a minimum of two copies of the minor allele seen in at least one of the four ancestry groups. The counts in (5) are less than (4) when there is more than one assay/feature for a given genomic position. The percentages given in (6) and (7) are with a denominator of unique positions, rather than unique assays. MAF, minor allele frequency.

  • a Product information. For Illumina arrays, number of samples (e.g., 4, 8, or 12), version of the array (e.g., “v1”), and version of the array manifest file (.bpm, e.g., “A” or “B”). For Affymetrix arrays, the NetAffx release number.